AutoCloner

Multiple sequence alignment - TraesCS3D01G160900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS3D01G160900	chr3D	100.000	2643	0	0	1	2643	131357386	131354744	0.000000e+00	4881.0
1	TraesCS3D01G160900	chr3B	92.838	2653	134	22	1	2643	187808817	187806211	0.000000e+00	3795.0
2	TraesCS3D01G160900	chr3B	86.923	130	16	1	447	575	235854430	235854301	7.620000e-31	145.0
3	TraesCS3D01G160900	chr3A	91.483	2313	108	31	337	2643	144157384	144155155	0.000000e+00	3097.0
4	TraesCS3D01G160900	chr3A	96.748	123	4	0	34	156	144162157	144162035	3.450000e-49	206.0
5	TraesCS3D01G160900	chr3A	84.828	145	9	6	198	329	144162035	144161891	1.650000e-27	134.0
6	TraesCS3D01G160900	chr5A	84.053	602	88	6	1934	2531	663947777	663948374	8.210000e-160	573.0
7	TraesCS3D01G160900	chr5A	80.967	331	48	5	1117	1436	663947248	663947574	5.650000e-62	248.0
8	TraesCS3D01G160900	chr5A	89.796	98	10	0	1511	1608	663947572	663947669	2.760000e-25	126.0
9	TraesCS3D01G160900	chr4D	85.255	373	48	6	1934	2302	483990382	483990751	6.910000e-101	377.0
10	TraesCS3D01G160900	chr7D	81.538	455	46	21	162	581	326053273	326052822	9.060000e-90	340.0
11	TraesCS3D01G160900	chr1D	82.508	303	38	9	144	438	207265845	207266140	4.370000e-63	252.0
12	TraesCS3D01G160900	chr1D	89.051	137	11	2	446	581	162062484	162062351	1.630000e-37	167.0
13	TraesCS3D01G160900	chr1A	91.241	137	11	1	446	581	222350478	222350614	4.490000e-43	185.0
14	TraesCS3D01G160900	chr1A	93.846	65	2	2	378	441	181760997	181760934	2.170000e-16	97.1
15	TraesCS3D01G160900	chr2A	91.129	124	11	0	447	570	270466941	270467064	4.520000e-38	169.0
16	TraesCS3D01G160900	chr2D	91.525	118	10	0	453	570	238158292	238158409	2.100000e-36	163.0
17	TraesCS3D01G160900	chr2D	88.679	106	10	1	155	260	238157741	238157844	7.680000e-26	128.0
18	TraesCS3D01G160900	chr4B	88.550	131	14	1	456	585	565737189	565737319	9.790000e-35	158.0
19	TraesCS3D01G160900	chr2B	88.710	124	14	0	447	570	297436495	297436618	4.560000e-33	152.0
20	TraesCS3D01G160900	chr4A	84.677	124	19	0	447	570	615515871	615515748	9.930000e-25	124.0
21	TraesCS3D01G160900	chr4A	95.238	63	2	1	378	440	358849668	358849607	6.020000e-17	99.0
22	TraesCS3D01G160900	chr7A	87.879	99	12	0	175	273	240725561	240725659	1.660000e-22	117.0
23	TraesCS3D01G160900	chr5B	95.312	64	2	1	378	441	112181948	112181886	1.670000e-17	100.0
24	TraesCS3D01G160900	chr5B	91.429	70	5	1	372	441	567784988	567785056	7.790000e-16	95.3

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS3D01G160900	chr3D	131354744	131357386	2642	True	4881.000000	4881	100.000000	1	2643	1	chr3D.!!$R1	2642
1	TraesCS3D01G160900	chr3B	187806211	187808817	2606	True	3795.000000	3795	92.838000	1	2643	1	chr3B.!!$R1	2642
2	TraesCS3D01G160900	chr3A	144155155	144157384	2229	True	3097.000000	3097	91.483000	337	2643	1	chr3A.!!$R1	2306
3	TraesCS3D01G160900	chr5A	663947248	663948374	1126	False	315.666667	573	84.938667	1117	2531	3	chr5A.!!$F1	1414

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
259	262	0.038455	AGCGGTGGAGTGACTAGTCT	59.962	55.0	23.01	4.29	0.0	3.24	F
1369	1388	0.104120	TCATGGATGCGTTAGGACCG	59.896	55.0	0.00	0.00	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1493	1512	0.312102	AAGCTGAAAAGTTGCTCCGC	59.688	50.0	0.00	0.00	35.85	5.54	R
2611	2652	4.685165	TCGAATGTTTACCGATCGAAAACA	59.315	37.5	32.02	32.02	44.56	2.83	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
56	57	6.822442	TGAATCGTATTAATACCAAGGCTGA	58.178	36.000	17.91	9.15	0.00	4.26
108	111	1.909700	TGTTTCTCCCTGACCATTGC	58.090	50.000	0.00	0.00	0.00	3.56
204	207	8.807118	AGTCTAGTAGTCTCAATTTGATTGTCA	58.193	33.333	0.00	0.00	41.02	3.58
217	220	5.845985	TTGATTGTCAACTAGCTTCTTCG	57.154	39.130	0.00	0.00	30.26	3.79
236	239	4.841443	TCGTGTAGACTAGCTTGTTGAA	57.159	40.909	1.43	0.00	0.00	2.69
250	253	1.202758	TGTTGAATTGAGCGGTGGAGT	60.203	47.619	0.00	0.00	0.00	3.85
255	258	1.557099	ATTGAGCGGTGGAGTGACTA	58.443	50.000	0.00	0.00	0.00	2.59
259	262	0.038455	AGCGGTGGAGTGACTAGTCT	59.962	55.000	23.01	4.29	0.00	3.24
260	263	0.889306	GCGGTGGAGTGACTAGTCTT	59.111	55.000	23.01	11.78	0.00	3.01
261	264	1.135344	GCGGTGGAGTGACTAGTCTTC	60.135	57.143	23.01	18.70	0.00	2.87
301	304	2.618053	GTCGATCGACTCAATTTGGGT	58.382	47.619	34.97	0.37	41.57	4.51
304	307	2.676750	CGATCGACTCAATTTGGGTGGA	60.677	50.000	15.29	15.29	39.86	4.02
305	308	3.545703	GATCGACTCAATTTGGGTGGAT	58.454	45.455	22.29	22.29	46.74	3.41
306	309	2.985896	TCGACTCAATTTGGGTGGATC	58.014	47.619	6.65	0.00	30.44	3.36
308	311	2.679837	CGACTCAATTTGGGTGGATCAG	59.320	50.000	6.65	0.00	26.09	2.90
334	339	0.936691	AGGGGAATTTGGGAGGGATG	59.063	55.000	0.00	0.00	0.00	3.51
351	356	4.411540	AGGGATGAGTGAGCAGTTGATTAT	59.588	41.667	0.00	0.00	0.00	1.28
381	386	6.994496	TCCACTTCCTGATGAAATAGCTATTG	59.006	38.462	19.53	6.05	31.06	1.90
500	506	5.382616	TGAGTACTATGGTACCATGTCGAT	58.617	41.667	33.41	18.19	46.81	3.59
565	571	1.009389	CAACCTTGGCTCGACTCGTC	61.009	60.000	0.00	0.00	0.00	4.20
584	590	7.481642	ACTCGTCGACTTGTAATTCTTGATAT	58.518	34.615	14.70	0.00	0.00	1.63
594	600	6.802608	TGTAATTCTTGATATCCGTCGACTT	58.197	36.000	14.70	0.80	0.00	3.01
603	609	7.500720	TGATATCCGTCGACTTGTAATTCTA	57.499	36.000	14.70	0.00	0.00	2.10
608	614	7.558161	TCCGTCGACTTGTAATTCTAGATAA	57.442	36.000	14.70	0.00	0.00	1.75
886	893	3.578688	GGTAGCACCTGCATTTGAAAAG	58.421	45.455	0.00	0.00	45.16	2.27
917	925	2.367894	TCAGATGCAGCTATCTCAAGGG	59.632	50.000	3.06	0.00	35.28	3.95
949	957	4.397103	CCTTTGCAAGATTGATCTGCTACA	59.603	41.667	0.00	1.48	37.19	2.74
973	981	9.747293	ACAGATTATAATGATGAGATATCAGCG	57.253	33.333	1.78	0.00	0.00	5.18
1110	1118	3.251571	ACAAAAGATAACCGACTCTCGC	58.748	45.455	0.00	0.00	38.82	5.03
1327	1346	1.337354	TGTTCGCTTAATGCCGAGACA	60.337	47.619	0.00	0.00	38.78	3.41
1336	1355	1.660167	ATGCCGAGACACATCACATG	58.340	50.000	0.00	0.00	0.00	3.21
1361	1380	0.821517	TCGTAAGGTCATGGATGCGT	59.178	50.000	0.00	0.00	38.47	5.24
1369	1388	0.104120	TCATGGATGCGTTAGGACCG	59.896	55.000	0.00	0.00	0.00	4.79
1453	1472	0.951558	TTCTTGAGAAACGCCTTGGC	59.048	50.000	0.75	0.75	0.00	4.52
1636	1655	1.201429	AGCCCTTACTCACCCCAGTG	61.201	60.000	0.00	0.00	46.00	3.66
1637	1656	1.299976	CCCTTACTCACCCCAGTGC	59.700	63.158	0.00	0.00	44.16	4.40
1638	1657	1.299976	CCTTACTCACCCCAGTGCC	59.700	63.158	0.00	0.00	44.16	5.01
1648	1667	1.252904	CCCCAGTGCCCTGATTGTTG	61.253	60.000	0.00	0.00	41.50	3.33
1649	1668	0.540365	CCCAGTGCCCTGATTGTTGT	60.540	55.000	0.00	0.00	41.50	3.32
1654	1673	0.831288	TGCCCTGATTGTTGTTGGGG	60.831	55.000	0.00	0.00	38.34	4.96
1726	1745	5.235850	TGTCTAGTTTATCAACCCAGCAA	57.764	39.130	0.00	0.00	32.70	3.91
1727	1746	5.001232	TGTCTAGTTTATCAACCCAGCAAC	58.999	41.667	0.00	0.00	32.70	4.17
1789	1809	3.056607	GGCTGTTATGCAATCAACAACCT	60.057	43.478	17.68	0.00	37.72	3.50
1802	1822	9.294030	GCAATCAACAACCTTGATAAATAAGAG	57.706	33.333	0.00	0.00	38.11	2.85
1881	1901	3.740115	TCTTCACTTGCTGGTACCTTTC	58.260	45.455	14.36	2.61	0.00	2.62
1894	1914	1.342672	ACCTTTCTGTGTGGTCGGGT	61.343	55.000	0.00	0.00	0.00	5.28
1907	1927	1.472728	GGTCGGGTTATGCAATCTCGT	60.473	52.381	0.00	0.00	0.00	4.18
1920	1940	4.024472	TGCAATCTCGTCATTTCGTTTTGA	60.024	37.500	0.00	0.00	0.00	2.69
1969	2007	3.065925	GCAGATAGAACATTTGTGGCTCC	59.934	47.826	0.00	0.00	0.00	4.70
1974	2015	7.121168	CAGATAGAACATTTGTGGCTCCTTTTA	59.879	37.037	0.00	0.00	0.00	1.52
1982	2023	4.487714	TGTGGCTCCTTTTACTCATAGG	57.512	45.455	0.00	0.00	0.00	2.57
1991	2032	8.141909	GCTCCTTTTACTCATAGGTTTTGTTTT	58.858	33.333	0.00	0.00	0.00	2.43
2022	2063	2.878406	GCAGTTCAGTGGCAAAAGAGTA	59.122	45.455	0.00	0.00	0.00	2.59
2079	2120	3.003763	ACCCGAGTGGAGGCCTTC	61.004	66.667	6.77	4.87	37.49	3.46
2120	2161	6.284459	ACTACCAGAGAACAAAGAAAGACTG	58.716	40.000	0.00	0.00	0.00	3.51
2151	2192	3.225104	CACCTATTACCCTAGCGTGGTA	58.775	50.000	0.00	0.00	37.31	3.25
2160	2201	0.179108	CTAGCGTGGTAGAACTGGCC	60.179	60.000	0.00	0.00	0.00	5.36
2543	2584	3.516700	TGATGATGATCATGATAGGGCGT	59.483	43.478	14.30	0.00	37.20	5.68
2571	2612	6.530181	TGTGTTGTATATGAAGAAGCACTACG	59.470	38.462	0.00	0.00	0.00	3.51
2600	2641	7.206981	TGTTTTCTGTTTCAGGATCAGATTC	57.793	36.000	0.00	0.00	37.91	2.52
2610	2651	5.063204	TCAGGATCAGATTCAAACGTGTTT	58.937	37.500	0.00	0.00	0.00	2.83
2611	2652	5.530915	TCAGGATCAGATTCAAACGTGTTTT	59.469	36.000	0.00	0.00	0.00	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	4.898320	ACGATTCAATATGGAGCTATGCA	58.102	39.130	0.00	0.00	0.00	3.96
56	57	4.588899	TCCAACGTTTTCTGATCATCCAT	58.411	39.130	0.00	0.00	0.00	3.41
108	111	7.203910	AGAATCCTATTTGTGCTACTACGAAG	58.796	38.462	0.00	0.00	0.00	3.79
121	124	8.517878	CCATGGTTGCTATAAGAATCCTATTTG	58.482	37.037	2.57	0.00	0.00	2.32
138	141	2.877168	GAGACTCATCATCCATGGTTGC	59.123	50.000	16.72	3.35	32.64	4.17
166	169	6.663916	AGACTACTAGACTAGTCTCGCGACT	61.664	48.000	28.42	17.57	46.83	4.18
204	207	5.163733	GCTAGTCTACACGAAGAAGCTAGTT	60.164	44.000	0.00	0.00	30.13	2.24
217	220	6.401581	GCTCAATTCAACAAGCTAGTCTACAC	60.402	42.308	0.00	0.00	0.00	2.90
236	239	1.478510	CTAGTCACTCCACCGCTCAAT	59.521	52.381	0.00	0.00	0.00	2.57
259	262	6.645790	ACTCAAAAACCTAGACTAGTCGAA	57.354	37.500	17.07	8.80	34.09	3.71
260	263	6.251655	GACTCAAAAACCTAGACTAGTCGA	57.748	41.667	17.07	11.32	34.09	4.20
261	264	5.087397	CGACTCAAAAACCTAGACTAGTCG	58.913	45.833	17.07	6.00	45.90	4.18
301	304	4.965283	ATTCCCCTAAAAACCTGATCCA	57.035	40.909	0.00	0.00	0.00	3.41
304	307	4.782691	CCCAAATTCCCCTAAAAACCTGAT	59.217	41.667	0.00	0.00	0.00	2.90
305	308	4.140663	TCCCAAATTCCCCTAAAAACCTGA	60.141	41.667	0.00	0.00	0.00	3.86
306	309	4.164204	TCCCAAATTCCCCTAAAAACCTG	58.836	43.478	0.00	0.00	0.00	4.00
308	311	3.517901	CCTCCCAAATTCCCCTAAAAACC	59.482	47.826	0.00	0.00	0.00	3.27
334	339	6.317140	TGGATGAAATAATCAACTGCTCACTC	59.683	38.462	0.00	0.00	42.54	3.51
486	492	3.367321	TGGACTAATCGACATGGTACCA	58.633	45.455	18.99	18.99	0.00	3.25
487	493	3.799232	GCTGGACTAATCGACATGGTACC	60.799	52.174	4.43	4.43	0.00	3.34
500	506	4.547671	AGTCTAGGCTAATGCTGGACTAA	58.452	43.478	9.39	0.00	38.85	2.24
565	571	6.129431	CGACGGATATCAAGAATTACAAGTCG	60.129	42.308	4.83	0.00	38.99	4.18
566	572	6.916387	TCGACGGATATCAAGAATTACAAGTC	59.084	38.462	4.83	0.00	0.00	3.01
567	573	6.696148	GTCGACGGATATCAAGAATTACAAGT	59.304	38.462	0.00	0.00	0.00	3.16
568	574	6.918569	AGTCGACGGATATCAAGAATTACAAG	59.081	38.462	10.46	0.00	0.00	3.16
569	575	6.802608	AGTCGACGGATATCAAGAATTACAA	58.197	36.000	10.46	0.00	0.00	2.41
570	576	6.387041	AGTCGACGGATATCAAGAATTACA	57.613	37.500	10.46	0.00	0.00	2.41
571	577	6.696148	ACAAGTCGACGGATATCAAGAATTAC	59.304	38.462	10.46	0.00	0.00	1.89
572	578	6.802608	ACAAGTCGACGGATATCAAGAATTA	58.197	36.000	10.46	0.00	0.00	1.40
584	590	7.066163	TGTTATCTAGAATTACAAGTCGACGGA	59.934	37.037	10.46	0.00	0.00	4.69
886	893	2.228343	AGCTGCATCTGAACTCTTTTGC	59.772	45.455	1.02	0.00	0.00	3.68
917	925	4.460382	TCAATCTTGCAAAGGACATTCTCC	59.540	41.667	0.00	0.00	46.24	3.71
973	981	4.491676	TGCTTTCATAGGACAGTCGTTAC	58.508	43.478	0.05	0.00	0.00	2.50
1002	1010	0.533755	AATAGCCAGCATCGTCAGCC	60.534	55.000	0.00	0.00	0.00	4.85
1327	1346	4.191544	CCTTACGATTGACCATGTGATGT	58.808	43.478	0.00	0.00	0.00	3.06
1336	1355	3.536956	TCCATGACCTTACGATTGACC	57.463	47.619	0.00	0.00	0.00	4.02
1361	1380	0.907704	AGCACACCATCCGGTCCTAA	60.908	55.000	0.00	0.00	44.71	2.69
1369	1388	4.440525	CCAATGTTTATGAGCACACCATCC	60.441	45.833	0.00	0.00	0.00	3.51
1404	1423	2.158623	ACAAGCTCAGGTTCATCCACAA	60.159	45.455	0.00	0.00	39.02	3.33
1453	1472	2.749044	ACATCAAGGCCTGCTGCG	60.749	61.111	5.69	0.00	42.61	5.18
1493	1512	0.312102	AAGCTGAAAAGTTGCTCCGC	59.688	50.000	0.00	0.00	35.85	5.54
1495	1514	6.743575	TTATCTAAGCTGAAAAGTTGCTCC	57.256	37.500	0.00	0.00	35.85	4.70
1552	1571	2.420628	TTGCCTTGCATGTTTCTTCG	57.579	45.000	0.00	0.00	38.76	3.79
1636	1655	0.831711	ACCCCAACAACAATCAGGGC	60.832	55.000	0.00	0.00	38.14	5.19
1637	1656	0.968405	CACCCCAACAACAATCAGGG	59.032	55.000	0.00	0.00	40.58	4.45
1638	1657	0.318120	GCACCCCAACAACAATCAGG	59.682	55.000	0.00	0.00	0.00	3.86
1654	1673	1.826385	AACTGCTAACATCTGGGCAC	58.174	50.000	0.00	0.00	0.00	5.01
1726	1745	5.304101	TCAAAAACAATAACCAGCCAGATGT	59.696	36.000	0.00	0.00	0.00	3.06
1727	1746	5.782047	TCAAAAACAATAACCAGCCAGATG	58.218	37.500	0.00	0.00	0.00	2.90
1735	1754	9.829507	ATTGATGTCTTTCAAAAACAATAACCA	57.170	25.926	0.00	0.00	38.98	3.67
1764	1784	4.374843	TGTTGATTGCATAACAGCCATC	57.625	40.909	7.39	0.00	37.23	3.51
1789	1809	8.806429	TTGGAACTGATGCTCTTATTTATCAA	57.194	30.769	0.00	0.00	0.00	2.57
1802	1822	4.278419	ACTGTAAACCTTTGGAACTGATGC	59.722	41.667	0.00	0.00	0.00	3.91
1881	1901	0.321210	TGCATAACCCGACCACACAG	60.321	55.000	0.00	0.00	0.00	3.66
1894	1914	5.794687	AACGAAATGACGAGATTGCATAA	57.205	34.783	0.00	0.00	37.03	1.90
1982	2023	8.447053	TGAACTGCAAAAAGGATAAAACAAAAC	58.553	29.630	0.00	0.00	0.00	2.43
1991	2032	3.255642	GCCACTGAACTGCAAAAAGGATA	59.744	43.478	0.00	0.00	0.00	2.59
1992	2033	2.036346	GCCACTGAACTGCAAAAAGGAT	59.964	45.455	0.00	0.00	0.00	3.24
1993	2034	1.408702	GCCACTGAACTGCAAAAAGGA	59.591	47.619	0.00	0.00	0.00	3.36
1994	2035	1.136695	TGCCACTGAACTGCAAAAAGG	59.863	47.619	0.00	0.00	30.85	3.11
2022	2063	3.882326	CCCAGCCCGATGATGCCT	61.882	66.667	0.00	0.00	0.00	4.75
2079	2120	2.386661	AGTAGTTGACTGGGCAATCG	57.613	50.000	0.00	0.00	36.87	3.34
2120	2161	1.071857	GGTAATAGGTGTAGCTGGGGC	59.928	57.143	0.00	0.00	39.06	5.80
2151	2192	2.555547	GCTGTTTGCGGCCAGTTCT	61.556	57.895	2.24	0.00	41.02	3.01
2543	2584	5.411361	GTGCTTCTTCATATACAACACACCA	59.589	40.000	0.00	0.00	0.00	4.17
2571	2612	7.173907	TCTGATCCTGAAACAGAAAACATCTTC	59.826	37.037	0.00	0.00	37.66	2.87
2610	2651	5.177142	TCGAATGTTTACCGATCGAAAACAA	59.823	36.000	32.80	22.25	43.90	2.83
2611	2652	4.685165	TCGAATGTTTACCGATCGAAAACA	59.315	37.500	32.02	32.02	44.56	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.